Modeling convection-diffusion-reaction systems for microfluidic molecular communications with surface-based receivers in Internet of Bio-Nano Things.

We consider a microfluidic molecular communication (MC) system, where the concentration-encoded molecular messages are transported via fluid flow-induced convection and diffusion, and detected by a surface-based MC receiver with ligand receptors placed at the bottom of the microfluidic channel. The overall system is a convection-diffusion-reaction system that can only be solved by numerical methods, e.g., finite element analysis (FEA). However, analytical models are key for the information and communication technology (ICT), as they enable an optimisation framework to develop advanced communication techniques, such as optimum detection methods and reliable transmission schemes. In this direction, we develop an analytical model to approximate the expected time course of bound receptor concentration, i.e., the received signal used to decode the transmitted messages. The model obviates the need for computationally expensive numerical methods by capturing the nonlinearities caused by laminar flow resulting in parabolic velocity profile, and finite number of ligand receptors leading to receiver saturation. The model also captures the effects of reactive surface depletion layer resulting from the mass transport limitations and moving reaction boundary originated from the passage of finite-duration molecular concentration pulse over the receiver surface. Based on the proposed model, we derive closed form analytical expressions that approximate the received pulse width, pulse delay and pulse amplitude, which can be used to optimize the system from an ICT perspective. We evaluate the accuracy of the proposed model by comparing model-based analytical results to the numerical results obtained by solving the exact system model with COMSOL Multiphysics

Maximum Likelihood Detection With Ligand Receptors for Diffusion-Based Molecular Communications in Internet of Bio-Nano Things.

Molecular Communication (MC) is a bio-inspired communication technique that uses molecules as a method of information transfer among nanoscale devices. MC receiver is an essential component having profound impact on the communication system performance. However, the interaction of the receiver with information bearing molecules has been usually oversimplified in modeling the reception process and developing signal detection techniques. In this paper, we focus on the signal detection problem of MC receivers employing receptor molecules to infer the transmitted messages encoded into the concentration of molecules, i.e., ligands. Exploiting the observable characteristics of ligand-receptor binding reaction, we first introduce a Maximum Likelihood (ML) detection method based on instantaneous receptor occupation ratio, as aligned with the current MC literature. Then, we propose a novel ML detection technique, which exploits the amount of time the receptors stay unbound in an observation time window. A comprehensive analysis is carried out to compare the performance of the detectors in terms of bit error probability. In evaluating the detection performance, emphasis is given to the receptor saturation problem resulting from the accumulation of messenger molecules at the receiver as a consequence of intersymbol interference. The results reveal that detection based on receptor unbound time is quite reliable even in saturation, whereas the reliability of detection based on receptor occupation ratio substantially decreases as the receiver gets saturated. Finally, we also discuss the potential methods of implementing the detectors

Transmitter and Receiver Architectures for Molecular Communications: A Survey on Physical Design with Modulation, Coding, and Detection Techniques

Inspired by nature, molecular communications (MC), i.e., the use of molecules to encode, transmit, and receive information, stands as the most promising communication paradigm to realize the nanonetworks. Even though there has been extensive theoretical research toward nanoscale MC, there are no examples of implemented nanoscale MC networks. The main reason for this lies in the peculiarities of nanoscale physics, challenges in nanoscale fabrication, and highly stochastic nature of the biochemical domain of envisioned nanonetwork applications. This mandates developing novel device architectures and communication methods compatible with MC constraints. To that end, various transmitter and receiver designs for MC have been proposed in the literature together with numerable modulation, coding, and detection techniques. However, these works fall into domains of a very wide spectrum of disciplines, including, but not limited to, information and communication theory, quantum physics, materials science, nanofabrication, physiology, and synthetic biology. Therefore, we believe it is imperative for the progress of the field that an organized exposition of cumulative knowledge on the subject matter can be compiled. Thus, to fill this gap, in this comprehensive survey, we review the existing literature on transmitter and receiver architectures toward realizing MC among nanomaterial-based nanomachines and/or biological entities and provide a complete overview of modulation, coding, and detection techniques employed for MC. Moreover, we identify the most significant shortcomings and challenges in all these research areas and propose potential solutions to overcome some of them.This work was supported in part by the European Research Council (ERC) Projects MINERVA under Grant ERC-2013-CoG #616922 and MINERGRACE under Grant ERC-2017-PoC #780645

Nano/Bio-Receiver Architectures and Detection Methods for Molecular Communications

Internet of Nano Things (IoNT) is an emerging technology, which aims at extending the connectivity into nanoscale and biological environments with collaborative networks of artificial nanomachines and biological entities integrated into the Internet. To enable the IoNT and its groundbreaking applications, such as real-time intrabody health monitoring, it is imperative to devise nanoscale communication techniques with low-complexity transceiver architectures. Bio-inspired molecular communications (MC), which uses molecules to transfer information, is the most promising technique to realise IoNT due to its inherent biocompatibility and reliability in physiologically-relevant environments. Despite the substantial body of work concerning MC, the implications of an interface between MC channel and practical MC transceiver architectures are largely neglected, leading to a major gap between theory and practice. As the first step to remove this discrepancy, in this thesis, I develop a realistic analytical ICT model for microfluidic MC with surface-based receivers as a convection-diffusion-reaction system. In the second part, I focus on biological MC receivers, which can be implemented in living cells using synthetic biology tools. In this direction, I theoretically develop low-complexity and reliable MC detection methods exploiting the various statistics of the stochastic ligand-receptor interactions at the membrane of biological MC receivers. The estimation and detection theoretical analysis of these detection methods demonstrate that even single type of receptors can provide sufficient statistics to overcome the receptor saturation problem, cope with the interference of non-cognate molecules, and simultaneously sense the concentration of multiple types of ligands. I also propose synthetic receptor designs for the transduction of decision statistics into a representation by concentration of intracellular molecules, and design chemical reaction networks performing decoding with intracellular reactions. Finally, I fabricate a micro/nanoscale MC receiver based on graphene field-effect transistor biosensors and perform its ICT characterisation in a custom-designed microfluidic MC system with the information encoded into the concentration of DNAs. This experimental platform is the first practical demonstration of micro/nanoscale MC, and can serve as a testbed for developing realistic MC methods

Frequency-Domain Model of Microfluidic Molecular Communication Channels with Graphene BioFET-based Receivers

Molecular Communication (MC) is a bio-inspired communication paradigm utilizing molecules for information transfer. Research on this unconventional communication technique has recently started to transition from theoretical investigations to practical testbed implementations, primarily harnessing microfluidics and sensor technologies. Developing accurate models for input-output relationships on these platforms, which mirror real-world scenarios, is crucial for assessing modulation and detection techniques, devising optimized MC methods, and understanding the impact of physical parameters on performance. In this study, we consider a practical microfluidic MC system equipped with a graphene field effect transistor biosensor (bioFET)-based MC receiver as the model system, and develop an analytical end-to-end frequency-domain model. The model provides practical insights into the dispersion and distortion of received signals, thus potentially informing the design of new frequency-domain MC techniques, such as modulation and detection methods. The accuracy of the developed model is verified through particle-based spatial stochastic simulations of pulse transmission in microfluidic channels and ligand-receptor binding reactions on the receiver surface

Молекулярні антени на основі силікатів кальцію для біотехніки

Роботу викладено на 93 сторінках, вона містить 5 розділів, 25 ілюстрацій, 26 таблиць і 70 джерел в переліку посилань. Об’єктом дослідження є пластини кремнія n-типу провідності для виготовлення композитної біосумісної структури. Предметом дослідження є силікат кальцію на підкладинці кремнію для створення молекулярних антен. Метою роботи є створення сенсорів біологічних речовин на основі кремнієвого польового транзистора (BioFET). Отримана композитна структура Si/SiO2/(CaO-SiO2), яка демонструє властивість біосумісності, що підтверджено утворенням гідроксиапатиту на поверхні Si після зберігання в розчині, що імітує плазму крові людини. У першому інформаційно-аналітичному розділі роботи визначено необхідність вивчення та удосконалення комунікації і взаємодії на базі обмінюваної інформації елементів Інтернету біо- наноречей. У другому інформаційно- аналітичному розділі роботи наведено сучасний стан розвитку біотехнології та зокрема біопольових транзисторів. У третьому розділі наведена теоретична модель роботи молекулярної антени на основі біопольового транзистора. У четвертому розділі вивчається композитна структура Si/SiO2/(CaOSiO2) на поверхні кремнію, яка була синтезована методом сонохімічного синтезу та подальшим утворенням гідроксиапатиту при вимочуванні зразка в рідині, що симулює плазму людської крові. У п'ятому розділі представлений розроблений стартап-проект на основі досліджень по виконаній роботі.The work was found on 93 pages, it contained 5 sections, 25 images, 26 persons and 70 sources in translation. The object of the study is n-type silicon wafers for the manufacture of composite biocompatible structures. The subject of the study is calcium silicate on a silicon substrate to create molecular antennas. The method of operation creates a sensitive biological potential on a large silicon transistor (BioFET). The obtained Si/SiO2/(CaO-SiO2) composite structure demonstrates the power of biological ability, which confirms the formation of hydroxyapatite at the level of Si after being preserved in the section requiring human creep. In the first information and analytical section of the work, the reliability and improvement of communications were achieved, and we see information from the Internet of bio-things on the basis of exchange data. In another information and analytical section are the current state of development of biotechnology and such biofield transistors. The third section deals with the analytical model of the operation of a molecular antenna on a biological transistor. The fourth section examines the composite structure of Si/SiO2/(CaOSiO2) on the silicon surface, which was synthesized by sonochemical synthesis and the subsequent formation of hydroxyapatite when soaking the sample in a fluid simulating human blood plasma. The fifth section presents a developed startup project based on research on the work done

Silica and Silicon Based Nanostructures

Silica and silicon-based nanostructures are now well-understood materials for which the technologies are mature. The most obvious applications, such as electronic devices, have been widely explored over the last two decades. The aim of this Special Issue is to bring together the state of the art in the field and to enable the emergence of new ideas and concepts for silicon and silica-based nanostructures